serac: a R package for ShortlivEd RAdionuclide Chronology of recent sediment cores

Rosalie Bruel
April 5^th, 2019

Content

I had to produce some age-depth model plot for my PhD thesis. My colleagues working on dating would usually use a spreadsheet, and then a paying photo editor to edit their figures. I do not have the license for either of these, so of course I turned to R. My colleague Pierre Sabatier thought it was great and that we should turn the code in something even more automatic.

1. Get your data

We are sharing within the package data from Lake Allos (France), so users can follow along. The publication by Wilhelm et al (2012) is accessible here.

left: Lake Allos (Source: Flickr); right: Location, hydrological, geological and geomorphological characteristics of Lake Allos and its catchment (Fig. 1 in Wilhelm et al 2012)

Your dataset should follow a similar format than the one below.

2. Download serac

You can download serac from my GitHub repository using the packages devtools.

3. Test your hypotheses

At the minimum, your function will be:

serac(name="ALO09P12",coring_yr=2009)


 Sedimentation rate (CFCS model): V= 1.197mm/yr, R2= 0.9597
                          Error:     +/- 0.053mm/yr
 Inventory (Lead): 11707.91 Bq/m2 (range: 11176-12240 Bq/m2)
 Inventory (Cesium): 21549.328 Bq/m2 (range: 21405-21694 Bq/m2)



 ________________________

 The calculation took 0.856 seconds.

Several sedimentation hypotheses were tested, and this is what the author chose as the best model:

serac(name="ALO09P12",coring_yr=2009,model=c("CFCS"),plotphoto=FALSE,minphoto=c(0),maxphoto=c(210),plot_Pb=T,plot_Am=T,plot_Cs=T,Cher=c(30,40),Hemisphere=c("NH"),NWT=c(51,61),sedchange=c(75.5),plot_Pb_inst_deposit=T,inst_deposit=c(20,28,100,107,135,142,158,186),suppdescriptor=TRUE,descriptor_lab=c("Ca/Fe"),historic_d=c(20,28,100,107,135,142,158,186),historic_a=c(1994,1920,1886,1868),historic_n=c("sept1 994 flood","1920 flood","1886 flood","1868 flood ?"), min_yr=c(1750),dmax=c(180), plotpdf=TRUE,preview=F)


 Sedimentation rate (CFCS model) 0-75.5mm: V= 1.096mm/yr, R2= 0.9451
                          Error:     +/- 0.088mm/yr

 Sedimentation rate (CFCS model) 75.5mm-bottom: V= 0.796mm/yr, R2= 0.9226
                          Error:     +/- 0.082mm/yr
 Approximation of age at change(s) in sedimentation rate:
     Best Age: 1947 (incertitude: 1942-1952)


 Age approximation of instantaneous deposit(s) from CFCS model:
     The instantaneous deposit at 20-28 mm has an estimated range of: 1989-1992.

     The instantaneous deposit at 100-107 mm has an estimated range of: 1905-1928.

     The instantaneous deposit at 135-142 mm has an estimated range of: 1866-1897.

     The instantaneous deposit at 158-186 mm has an estimated range of: 1844-1879.

 Inventory (Lead): 10287.66 Bq/m2 (range: 9828-10748 Bq/m2)
 Inventory (Cesium): 19023.688 Bq/m2 (range: 18895-19153 Bq/m2)


 ________________________

 The calculation took 0.443 seconds.

Source

Table of content created using this method.